So I know the real world parallel rationale for Khan was the Joker
Eh.. what ?
Both people here and the writers made comparisons between this sequel and the Dark Knight before the movie was released. The correlation to gather from that was that the writers were going to pick a villain who was comparable to the Joker. There really isn't one, but the closest thing to a memorable villain to the general public (at least for the original series) was Khan.
Both characters somewhat represent the bottom of the bag of tricks. Not many other characters will have as much of a draw, if that's the ultimate goal.
Yet everyone keeps asking this question of "How do you top Khan?" as if it absolutely has to be topped. Batman didn't bother to do it. They didn't pick a villain that was known to the public, and they didn't try and top anything. They just tried to tell a story that fit in with how they pictured their trilogy to work.
I'm guessing this is where the Batman analogies will stop.